The story begins when Garrett is paired with his former apprentice, Erin, with both accepting the same job from their contact Basso. On their way there, Garrett steals Erin's claw without her noticing, because she usually uses it to kill guards when not necessary. They arrive at their job's location, Baron Northcrest's manor, and find a ritual taking place. Garrett gets a bad feeling and calls off the job, but Erin disagrees. They struggle on the rooftop and she ends up falling into the center of the ritual, which was nearing its completion. Erin stops and floats in mid-air as she is surrounded by the ritual's energy. A part of the building falls on Garrett, knocking him out. When he awakens we learn that he has been gone for a year, and The City is being plagued by a disease of unknown origin known as "The Gloom" and that the Baron had put The City in lockdown because of it. Back to his hideout, Garrett is hired by Basso to steal a ring from a man named Cornelius who died recently, and sneaks into a foundry where the victims of the Gloom are being disposed of. Just as Garrett grabs the ring he is discovered by the Baron's right-hand man, the Thief-Taker General, and flees. After completing the job, Garrett is introduced to Orion, a man who leads the resistance against the Baron's tyranny and hires him to infiltrate the "House of Blossoms" brothel in search for an ancient book. Before sneaking into the brothel, Garrett pays a visit to Erin's hideout where he has some visions of her mentioning the Moira Asylum. At the House of Blossoms, Garrett finds the entrance to an ancient library where he retrieves the book, and confronts the General and his men on his way back to the surface. Upon learning that Basso has been arrested and imprisoned inside the Baron's Keep, Garrett infiltrates the keep and rescues Basso, but he decides to take advantage of the confusion to steal the contents of the Baron's most secret vault, where the General ambushes him. The thief escapes nonetheless, taking a piece from the Primal, the same mysterious stone he saw in the ritual one year before. The stone gives him another vision of Erin, revealing that she is still alive and under the influence of its power.
Garrett explores the Moira Asylum searching for clues about Erin where he finds the second piece of the stone but no signs of her whereabouts, and decides to confront the Baron at his manor, amid a revolution led by Orion to overthrow him. The Baron reveals that he intended to harness the power of the stone to use it into a new energy source, but when the ritual was interrupted, it unleashed the Gloom into The City, and Orion, who is revealed to be the Baron's illegitimate brother Aldous, took advantage of the chaos that ensued to arrange his downfall. After realizing that the final piece of the stone is embedded in Garrett's eye, the Baron drives him away, and the thief is informed by one of his informants, the Queen of Beggars, that the Primal stone must be reassembled and its power contained, not only for Erin's sake, but to save The City from the Gloom. Garrett then breaks into the old Cathedral where Orion is using Erin to heal the citizens, unaware that this 'cure' will eventually transform them into monsters. Once Garrett reaches Orion, the General appears and he has a final confrontation with him while Orion escapes with Erin. Garrett then follows Orion to his hideout, the ship known as the "Dawn's Light", where he attempts to dissuade him when Erin unleashes the power of the stone, killing Orion and attacking Garrett with it. In the end, Garrett succeeds in calming Erin and reassembles the stone, returning her to normal. The scene then cuts to the two of them on the ship in a reenactment of their original accident with Garrett struggling to save Erin from falling off the ship into the depths below. She slips from his grasp but this time he throws her the claw. There is a flash, and when Garrett awakens on the floor he finds the claw next to him, implying that Erin used it to climb back, but she is nowhere to be found.